/*
 * CodonFitnessFunction.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.evolution.wrightfisher;

import dr.evolution.datatype.AminoAcids;
import dr.evolution.datatype.Codons;
import dr.evolution.datatype.GeneticCode;
import dr.math.GammaDistribution;
import dr.math.MathUtils;

public class CodonFitnessFunction extends FitnessFunction {

	/**
	 * selection coefficients are gamma distributed with parameters alpha and beta
	 */
	public CodonFitnessFunction(int codonCount, double alpha, double beta, double pInv) {
		
		GammaDistribution gamma = new GammaDistribution(beta, alpha);
		stateSize = 20;
		
		fitness = new double[codonCount][stateSize];
		byte[] aaFittest = new byte[codonCount];
		fittest = getFittestGenome(codonCount, aaFittest);
		for (int i = 0; i < codonCount; i++) {
			
			fitness[i][aaFittest[i]] = 1.0;
			for (int j = 0; j < stateSize; j++) {
				
				if (j != aaFittest[i]) {

                    if (MathUtils.nextDouble() < pInv) {
                        fitness[i][j] = 0.0;
                    } else {

                        double prob = Math.round(MathUtils.nextDouble() * 1000.0)/1000.0;
                        while ((prob <= 0.0) || (prob >= 1.0)) {
                            prob = Math.round(MathUtils.nextDouble() * 1000.0)/1000.0;
                        }
                        fitness[i][j] = Math.max(0.0, 1.0 - gamma.quantile(prob));
                    }
				}
			}
		}
	}

	/**
	 * Assumes the sequence is represented as nucleotides
	 */
	public final double getFitness(byte[] sequence) {
		
		double totalFitness = 1.0;
		
		int count = 0;
		for (int i = 0; i < sequence.length; i+=3) {
			int codonState = (sequence[i] * 16) + (sequence[i+1] * 4) + sequence[i+2];
			//int codonState = codons.getState(sequence[i], sequence[i+1], sequence[i+2]);
	
			int aminoAcid = geneticCode.getAminoAcidState(codonState);
			
			//System.out.println(sequence[i] + "" + sequence[i+1] + "" + sequence[i+2] +"="+ AminoAcids.INSTANCE.getChar(aminoAcid));
			
			// stop codons are lethal of course
			if (aminoAcid < 0 || aminoAcid >= stateSize) {
				//System.out.println("Stop codon found! " + aminoAcid); 
				return 0.0;
			}
			totalFitness *= fitness[count][aminoAcid];
			if (totalFitness == 0.0) return 0.0;
			count += 1;
		}
		return totalFitness;
	}
	
	/**
	 * @return the relative fitness increase of the new state at given position to the old state.
	 */
	public double getFitnessFactor(int pos, byte newState, byte oldState) {
		throw new RuntimeException();
	}

	public final double[][] getFitnessTable() {
		
		for (int j = 0; j < fitness[0].length; j++) {
			for (int i = 0; i < fitness.length; i++) {
				System.out.print((Math.round(fitness[i][j]*1000.0)/1000.0)+"\t");
			}
			System.out.println();
		}
		
		return fitness;
	}
	
	public byte[] getFittestGenome(int codonCount, byte[] aa) {
		
		byte[] genome = new byte[codonCount*3];
		
		for (int i = 0; i < codonCount; i++) {
			
			int aminoAcid = stateSize;
			int pos1 = MathUtils.nextInt(4);
			int pos2 = MathUtils.nextInt(4);
			int pos3 = MathUtils.nextInt(4);
			int codonState = (pos1 * 16) + (pos2 * 4) + pos3;
			//int codonState = codons.getState(pos1, pos2, pos3);
			aminoAcid = geneticCode.getAminoAcidState(codonState);
					
			while (aminoAcid >= stateSize) {
				pos1 = MathUtils.nextInt(4);
				pos2 = MathUtils.nextInt(4);
				pos3 = MathUtils.nextInt(4);
				codonState = (pos1 * 16) + (pos2 * 4) + pos3;
				//codonState = codons.getState(pos1, pos2, pos3);
				aminoAcid = geneticCode.getAminoAcidState(codonState);
			}
			System.out.print(AminoAcids.INSTANCE.getChar(aminoAcid));
			
			genome[i*3] = (byte)pos1;
			genome[i*3+1] = (byte)pos2;
			genome[i*3+2] = (byte)pos3;
			aa[i] = (byte)aminoAcid;
		}
		System.out.println();
		
		return genome;
	}
		
	public void initializeToFittest(byte[] genome) {
		System.arraycopy(fittest, 0, genome, 0, fittest.length);
	}	
	
	int stateSize = 20;
	double[][] fitness;
	byte[] fittest = null;
	GeneticCode geneticCode = GeneticCode.UNIVERSAL; 
	Codons codons = Codons.UNIVERSAL;	
}